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Merge pull request miykael#4 from satra/updates
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updated basic notebooks
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@djarecka
djarecka committed Jul 30, 2017
2 parents 8f2828e + 272ac6d commit 682fc7c
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Showing 15 changed files with 1,461 additions and 1,614 deletions.
9 changes: 6 additions & 3 deletions notebooks/basic_configuration.ipynb
View file
Expand Up @@ -63,6 +63,9 @@
"outputs": [],
"source": [
"from nipype import config, logging\n",
"import os\n",
"os.makedirs('/output/log_folder', exist_ok=True)\n",
"os.makedirs('/output/crash_folder', exist_ok=True)\n",
"\n",
"config_dict={'execution': {'remove_unnecessary_outputs': 'true',\n",
" 'keep_inputs': 'false',\n",
Expand All @@ -71,13 +74,13 @@
" 'hash_method': 'timestamp',\n",
" 'local_hash_check': 'true',\n",
" 'create_report': 'true',\n",
" 'crashdump_dir': '/opt/tutorial/crash_folder',\n",
" 'crashdump_dir': '/output/crash_folder',\n",
" 'use_relative_paths': 'false',\n",
" 'job_finished_timeout': '5'},\n",
" 'logging': {'workflow_level': 'INFO',\n",
" 'filemanip_level': 'INFO',\n",
" 'interface_level': 'INFO',\n",
" 'log_directory': '/opt/tutorial/log_folder',\n",
" 'log_directory': '/output/log_folder',\n",
" 'log_to_file': 'true'}}\n",
"config.update_config(config_dict)\n",
"logging.update_logging(config)"
Expand Down Expand Up @@ -114,7 +117,7 @@
" 'filemanip_level' : 'DEBUG',\n",
" 'interface_level' : 'DEBUG',\n",
" 'log_to_file' : 'True',\n",
" 'log_directory' : '/opt/tutorial/log_folder'}"
" 'log_directory' : '/output/log_folder'}"
]
},
{
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60 changes: 30 additions & 30 deletions notebooks/basic_data_input.ipynb
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Expand Up @@ -80,7 +80,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 1,
"metadata": {
"collapsed": false,
"deletable": true,
Expand Down Expand Up @@ -131,7 +131,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 2,
"metadata": {
"collapsed": true,
"deletable": true,
Expand All @@ -155,7 +155,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 3,
"metadata": {
"collapsed": true,
"deletable": true,
Expand Down Expand Up @@ -189,7 +189,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 4,
"metadata": {
"collapsed": false,
"deletable": true,
Expand Down Expand Up @@ -229,7 +229,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 5,
"metadata": {
"collapsed": true,
"deletable": true,
Expand All @@ -255,7 +255,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 6,
"metadata": {
"collapsed": false,
"deletable": true,
Expand All @@ -266,8 +266,8 @@
"name": "stdout",
"output_type": "stream",
"text": [
"170727-19:13:54,954 workflow INFO:\n",
"\t Executing node datagrabber in dir: /tmp/tmpzh0nl8du/datagrabber\n"
"170730-12:25:32,161 workflow INFO:\n",
"\t Executing node datagrabber in dir: /tmp/tmplmop1pqt/datagrabber\n"
]
},
{
Expand All @@ -278,7 +278,7 @@
"func = /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz"
]
},
"execution_count": 10,
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -314,7 +314,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 7,
"metadata": {
"collapsed": false,
"deletable": true,
Expand Down Expand Up @@ -353,7 +353,7 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 8,
"metadata": {
"collapsed": false,
"deletable": true,
Expand All @@ -364,8 +364,8 @@
"name": "stdout",
"output_type": "stream",
"text": [
"170727-19:18:15,247 workflow INFO:\n",
"\t Executing node selectfiles in dir: /tmp/tmpkxrlth4a/selectfiles\n"
"170730-12:25:34,430 workflow INFO:\n",
"\t Executing node selectfiles in dir: /tmp/tmp5z9bopfl/selectfiles\n"
]
},
{
Expand All @@ -376,7 +376,7 @@
"func = /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz"
]
},
"execution_count": 13,
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -403,7 +403,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 9,
"metadata": {
"collapsed": false,
"deletable": true,
Expand All @@ -414,8 +414,8 @@
"name": "stdout",
"output_type": "stream",
"text": [
"170727-19:21:09,233 workflow INFO:\n",
"\t Executing node selectfiles in dir: /tmp/tmphih2czqa/selectfiles\n"
"170730-12:25:35,400 workflow INFO:\n",
"\t Executing node selectfiles in dir: /tmp/tmp59333sfs/selectfiles\n"
]
},
{
Expand All @@ -425,7 +425,7 @@
"anat = ['/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz', '/data/ds000114/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz']"
]
},
"execution_count": 15,
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -482,7 +482,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 10,
"metadata": {
"collapsed": true,
"deletable": true,
Expand Down Expand Up @@ -512,7 +512,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 11,
"metadata": {
"collapsed": false,
"deletable": true,
Expand Down Expand Up @@ -540,7 +540,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 12,
"metadata": {
"collapsed": false,
"deletable": true,
Expand All @@ -551,8 +551,8 @@
"name": "stdout",
"output_type": "stream",
"text": [
"170716-08:58:08,702 workflow INFO:\n",
"\t Executing node fssource in dir: /tmp/tmp9rd5qmlb/fssource\n"
"170730-12:25:39,247 workflow INFO:\n",
"\t Executing node fssource in dir: /tmp/tmpo_jxbjpx/fssource\n"
]
}
],
Expand All @@ -573,7 +573,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 13,
"metadata": {
"collapsed": false,
"deletable": true,
Expand All @@ -584,7 +584,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"aparc_aseg: ['/data/ds000114/derivatives/freesurfer/sub-01/mri/aparc+aseg.mgz', '/data/ds000114/derivatives/freesurfer/sub-01/mri/aparc.a2009s+aseg.mgz']\n",
"aparc_aseg: ['/data/ds000114/derivatives/freesurfer/sub-01/mri/aparc+aseg.mgz', '/data/ds000114/derivatives/freesurfer/sub-01/mri/aparc.a2009s+aseg.mgz', '/data/ds000114/derivatives/freesurfer/sub-01/mri/aparc.dktatlas+aseg.mgz']\n",
"\n",
"brainmask: /data/ds000114/derivatives/freesurfer/sub-01/mri/brainmask.mgz\n",
"\n",
Expand All @@ -611,7 +611,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 14,
"metadata": {
"collapsed": false,
"deletable": true,
Expand All @@ -622,8 +622,8 @@
"name": "stdout",
"output_type": "stream",
"text": [
"170716-08:58:55,407 workflow INFO:\n",
"\t Executing node fssource in dir: /tmp/tmp9rd5qmlb/fssource\n"
"170730-12:25:41,991 workflow INFO:\n",
"\t Executing node fssource in dir: /tmp/tmpo_jxbjpx/fssource\n"
]
}
],
Expand All @@ -644,7 +644,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 15,
"metadata": {
"collapsed": false,
"deletable": true,
Expand All @@ -657,7 +657,7 @@
"'/data/ds000114/derivatives/freesurfer/sub-01/surf/lh.inflated'"
]
},
"execution_count": null,
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
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